Transcriptome Analysis and Functional Identification of Xa13 and Pi-ta Orthologs in Oryza granulata.

Nees & Arn. ex Watt, a perennial wild rice species with a GG genome, preserves many important genes for cultivated rice ( L.) improvement. At present, however, no genetic resource is available for studying . Here, we report 91,562 high-quality transcripts of assembled de novo. Moreover, comparative transcriptome analysis revealed that 1311 single-copy orthologous pairs shared by and (Zoll. & Moritzi) Baill. that may have undergone adaptive evolution. We performed an analysis of the genes potentially involved in plant-pathogen interactions to explore the molecular basis of disease resistance, and isolated the full-length cDNAs of () and () orthologs from . The overexpression of in Nipponbare and functional characterization showed enhanced the resistance of transgenic Nipponbare to rice blast resulting from the presence of the gene. , an alternatively spliced transcript of the blast resistance gene in encodes a 1024-amino acid polypeptide with a C-terminal thioredoxin domain. This study provides an important resource for functional and evolutionary studies of the genus .

De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution.

The wild relatives of rice have adapted to different ecological environments and constitute a useful reservoir of agronomic traits for genetic improvement. Here we present the ~777 Mb de novo assembled genome sequence of Oryza granulata. Recent bursts of long-terminal repeat retrotransposons, especially RIRE2, led to a rapid twofold increase in genome size after O. granulata speciation. Universal centromeric tandem repeats are absent within its centromeres, while gypsy-type LTRs constitute the main centromere-specific repetitive elements. A total of 40,116 protein-coding genes were predicted in O. granulata, which is close to that of Oryza sativa. Both the copy number and function of genes involved in photosynthesis and energy production have undergone positive selection during the evolution of O. granulata, which might have facilitated its adaptation to the low light habitats. Together, our findings reveal the rapid genome expansion, distinctive centromere organization, and adaptive evolution of O. granulata.

Characterization of a new semi-dominant dwarf allele of SLR1 and its potential application in hybrid rice breeding.

The widespread introduction of semi-dwarf1 (sd1), also known as the 'Green Revolution' gene, has dramatically increased rice yield. However, the extensive use of limited sources of dwarf genes may cause 'bottleneck' effects in breeding new rice varieties. Alternative dwarf germplasms are quite urgent for rice breeding. Here, we characterized a new allele of the rice Slr1-d mutant, Slr1-d6, which reduced plant height by 37%, a much milder allele for dwarfism. Slr-d6 was still responsive to gibberellin (GA) to a reduced extent. The mutation site in Slr1-d6 was less conserved in the TVHYNP domain, leading to the specific semi-dominant dwarf phenotype. Expression of SLR1 and five key GA biosynthetic genes was disturbed in Slr1-d6, and the interaction between Slr1-d6 and GID1 was decreased. In the genetic background of cultivar 9311 with sd1 eliminated, Slr1-d6 homozygous plants were ~70 cm tall. Moreover, Slr1-d6 heterozygous plants were equivalent in height to the standard sd1 semi-dwarf 9311, but with a 25% yield increase, showing its potential application in hybrid rice breeding.